source: src/bondgraph.hpp@ 4b5cf8

/*
 * bondgraph.hpp
 *
 *  Created on: Oct 29, 2009
 *      Author: heber
 */

#ifndef BONDGRAPH_HPP_
#define BONDGRAPH_HPP_

using namespace std;

/*********************************************** includes ***********************************/

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <iosfwd>


/****************************************** forward declarations *****************************/

class molecule;
class BondedParticle;
class MatrixContainer;

/********************************************** definitions *********************************/

/********************************************** declarations *******************************/


class BondGraph {
public:
  /** Constructor of class BondGraph.
   * This classes contains typical bond lengths and thus may be used to construct a bond graph for a given molecule.
   */
  BondGraph(bool IsA);

  /** Destructor of class BondGraph.
   */
  ~BondGraph();

  /** Parses the bond lengths in a given file and puts them int a matrix form.
   * Allocates \a MatrixContainer for BondGraph::BondLengthMatrix, using MatrixContainer::ParseMatrix(),
   * but only if parsing is successful. Otherwise variable is left as NULL.
   * \param &input input stream to parse table from
   * \return true - success in parsing file, false - failed to parse the file
   */
  bool LoadBondLengthTable(std::istream &input);

  /** Creates the bond list for all atoms in a given molecule.
   * \param *mol molecule with atoms
   * \return true - success, false - failed to construct bond structure
   */
  bool CreateAdjacencyForMolecule(molecule * const mol);

  /** Returns the entry for a given index pair.
   * \param firstelement index/atom number of first element (row index)
   * \param secondelement index/atom number of second element (column index)
   * \note matrix is of course symmetric.
   */
  double GetBondLength(int firstelement, int secondelement);

  /** Determines the maximum of all element::CovalentRadius for elements present in \a *mol.
   * \param *out output stream for debugging
   * \param *mol molecule with all atoms and their respective elements.
   */
  double SetMaxDistanceToMaxOfCovalentRadii(const molecule * const mol);

  /** Returns bond criterion for given pair based on a bond length matrix.
   * This calls either the covalent or the bond matrix criterion.
   * \param *Walker first BondedParticle
   * \param *OtherWalker second BondedParticle
   * \param &MinDistance lower bond bound on return
   * \param &MaxDistance upper bond bound on return
   * \param IsAngstroem whether units are in angstroem or bohr radii
   */
  void getMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);

  /** Returns the maximum distance (e.g. necessary for LinkedCell).
   * \return BondGraph::max_distance
   */
  double getMaxDistance() const;

private:
  static const double BondThreshold;

  /** Returns bond criterion for given pair based on a bond length matrix.
   * The matrix should be contained in \a this BondGraph and contain an element-
   * to-element length.
   * \param *Walker first BondedParticle
   * \param *OtherWalker second BondedParticle
   * \param &MinDistance lower bond bound on return
   * \param &MaxDistance upper bond bound on return
   * \param IsAngstroem whether units are in angstroem or bohr radii
   */
  void BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);

  /** Returns bond criterion for given pair based on covalent radius.
   * \param *Walker first BondedParticle
   * \param *OtherWalker second BondedParticle
   * \param &MinDistance lower bond bound on return
   * \param &MaxDistance upper bond bound on return
   * \param IsAngstroem whether units are in angstroem or bohr radii
   */
  void CovalentMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem);

  //!> Matrix with bond lenth per two elements
  MatrixContainer *BondLengthMatrix;
  //!> maximum distance over all bonds possible
  double max_distance;
  //!> distance units are angstroem (true), bohr radii (false)
  bool IsAngstroem;
};

#endif /* BONDGRAPH_HPP_ */